The aim of this study was to establish the seasonal variation of fungal propagules in homes of Mérida, Mexico, and to examine the relation between their concentrations in enclosed and open locations taking into account environmental parameters such as temperature, humidity and wind speed. Samples were taken inside and outside domestic environments during the most characteristic weather seasons in the region: dry season (sampled in May), rainy season (sampled in October), and cold fronts season (sampled in February). The geometric mean of the indoors and outdoors concentration of airborne fungal propagules was 1653 and 1432 CFU/m3 during the cold fronts period, 125 and 92 CFU/m3 during the dry period, and 1326 and 1145 CFU/m3 during the rainy period. The respirable fraction during the three periods sampled was always within a range of 50 to 100%. The composition of fungal genera exhibited a seasonal change, and 19 of these were identified. The main genera found during the three periods were Cladosporium spp., Penicillium spp., Aspergillus spp., Fusarium spp., andAcremonium spp. The fungal aerosol concentrations and diversity found in Mérida, Mexico, were similar to those from other reports of cities with comparable tropical humid climate. This study concludes that the concentration of airborne fungal propagules and its respirable fraction can be related to several meteorological factors, mainly to relative humidity